diff --git a/cami_src/cami_suite.py b/cami_src/cami_suite.py index a7df6f7a18a41010cd5d3fd4b2a65a4dc08d9c0c..4825d6261b9f7280bd17d38c8c225a9ab085e8c2 100644 --- a/cami_src/cami_suite.py +++ b/cami_src/cami_suite.py @@ -342,7 +342,7 @@ class cami(): # transform all vertex indices to their corresponding gene names in a result set for tool in result_sets: self.result_gene_sets[tool.name] = set([gene_name_map[vertex] for vertex in result_sets[tool]]) - + # create integer codes for cami_versions (needed for predicted_by vertex property) recursion_limit = sys.getrecursionlimit() for cami_method_name, cami_params in camis.items(): @@ -374,20 +374,15 @@ class cami(): # for visualization with nvenn self.result_gene_sets[cami_method_name] = set(cami_genes) - - # transform all vertex indices to their corresponding gene names in a result set - for tool in result_sets: - self.result_gene_sets[tool.name] = set([gene_name_map[vertex] for vertex in result_sets[tool]]) - - # add seeds to result sets for drugstone and digest - for toolname in self.result_gene_sets: - self.result_module_sets[toolname] = self.result_gene_sets[toolname].union(set([gene_name_map[svertex] for svertex in self.seed_lst])) - print(f'With the {len(seed_genes)} seed genes the module predicted by {toolname} contains {len(self.result_module_sets[toolname])} genes') - sys.setrecursionlimit(recursion_limit) # save the results in outputfiles self.generate_output(cami_method_name, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes, gene_name_map, codes2tools, cami_scores) + + # add seeds to result sets for drugstone and digest + for toolname in self.result_gene_sets: + self.result_module_sets[toolname] = self.result_gene_sets[toolname].union(set([gene_name_map[svertex] for svertex in self.seed_lst])) + print(f'With the {len(seed_genes)} seed genes the module predicted by {toolname} contains {len(self.result_module_sets[toolname])} genes') def generate_output(self, cami_method, seed_genes, cami_vlist, cami_vertices, putative_vertices, cami_genes, gene_name_map, codes2tools, cami_scores):